João Rodrigues

🚨 Super excited for our new preprint on flexibility cues in AlphaFold!

Together with @ezgikaraca.bsky.social and @aysebercinb.bsky.social, we found that distograms of AF2.3 and AF3 mirror MD sampling by predicting the extent of a novel conformational change! 🤯

For more👇

We just bumped into something very preliminary… but very exciting:

AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.

Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...

CAPRI Docking

A small reminder to all structural biologists around working on biomolecular complexes: please consider sharing your complexes as targets for CAPRI - AI has not solved all structure prediction problems and there are still challenges! See www.capri-docking.org/contribute/

Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps www.biorxiv.org/content/10.1101/2025.07.25.666757v1 #cryoEM

Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes Motivation: AlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without co-evolutionary signals, such as host-pathogen and a...

A paper thar took too long to finish. We show that AlphaFold3 its clearly better than AlphaFold2 (and Boltz-1 and Chai-1) to predict the structure of antibody-Antigens, but only for cases with (har to detect) similarity in the training set.

www.biorxiv.org/content/10.1...

Happy to share that our paper on Metric Ion Classification (MIC) is now published!

www.nature.com/articles/s41...

Calling all structural biologists in the NYC metro area! The nysbdg.bsky.social is back for in-person events!

Register here 👉🏼 buff.ly/dGmJeau

I look forward to seeing you there! 😎

#structuralbiology #cyrstallography #cryoEM #NMR
#chromatography #proteinpurification #AKTAsystems

Postdoctoral Scientist - Structural Studies - Dr Joe Greener - LMB 2633 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840475 Postdoctoral Scientist Salary £41,344 per annum  Fixed Term – 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postd...

Interested in a postdoc position combining computational protein design and molecular simulation? There is an open position in my group at the MRC-LMB in Cambridge, UK.

www.nature.com/naturecareer...

Feel free to message me with any questions.

With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp

Only a few days left to apply for our EMBO course with a great lineup of speakers and tutors! Please feel free to RT!

Course website: meetings.embo.org/event/25-bio...

Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social

Location: www.ibg.edu.tr

To put it simply, Europe funds education, the US funds research.

I get it. I was trying to make the point that Europe simply cannot make up for those cuts because it's a fundamentally different system.. in my opinion, making any type of comparisons is pointless.

And yet ~50% of postdocs in the US are foreigners :) I wouldn't compare different systems, built on societies with different sets of values. If Europe (et al) invests more as a result of US divestment, that's a net positive: more diversity of ideas, less concentration of IP, the list goes on..

New paper out www.frontiersin.org/journals/bio...

VTX is available at github.com/VTX-Molecula...

@cg-martini.bsky.social @janstevens.bsky.social

@maximemaria.bsky.social @sguionni.bsky.social @pltc.bsky.social @qubit-pharma.bsky.social

The rendering style got me half expecting to see Goku and Vegeta pop up at any moment from behind a helix! Beautiful! Great job!!

This paper combines two sort-of-crazy (in the best sense) approaches in cryoEM sample preparation:
(1) Native, soft-landing electrospray ion beam deposition, followed by (2) deposition of amorphous ice, and reheating and freezing by laser flash melting. Has potential for time-resolved studies.

Depending on where you'll be, try and look for local cycling/wheelers clubs. They're usually nice, organize rides, etc. A quick search for Boston shows www.crw.org which actually seems really nice!

Ah! Tomayto, tomahto 😜

Really cool work on diffusing structures into cryo-EM densities by Ellen Zhong et. al arxiv.org/html/2506.04...

#cryoem

Several bar plots showing the improved performance and ability to generalize to unseen targets of Diffdock-Glide vs standard Diffdock.

New preprint from my colleagues at Schrödinger on blending ML methods with physics-based refinement and scoring to improve small molecule docking performance - and generalization - on several tasks for early stages of drug discovery. Link👇

www.biorxiv.org/content/10.1...

#chemsky

The manuscript describing the new modular version of HADDOCK is finally available as a preprint! The result of a team work over several years, supported by @bioexcelcoe.bsky.social @bijvoet-centre.bsky.social @esciencecenter.bsky.social - www.biorxiv.org/content/10.1...

This has been a long journey, but it's now out in final form. @kjamali.bsky.social

academic.oup.com/bioinformati...

Anybody know on TED (The Encyclopedia of Domains), what the domain-domain "Interaction score" is? I can't find it in the paper on or on the website. Example: kinase N and C terminal domains for EGFR have a score of 7.0:

ted.cathdb.info/uniprot/P00533

You can send me an email at firstname.lastname@schrodinger.com, or DM me here, or LinkedIn, whatever you prefer!

Enabling cryoEM structures for drug discovery with the Schrödinger Suite - Schrödinger In drug discovery, the relevance and value of protein structures is directly related to their ability to rationally optimize molecular properties.

My team at Schrödinger is looking for 2 interns to join us in NYC for 3 months this summer!

If you are comfortable writing Python, know (even a little!) about protein structure, and can work in the US, feel free to reach out!

Check the kind of work we do 👇

tinyurl.com/43j57uww

Hear from some of our past GSoC contributors

Google Summer of Code projects are available this year to improve molecular simulation in Molly.jl.

Feel free to ask me any questions.

julialang.org/jsoc

YouTube video by SBGrid Consortium Schrödinger

Many thanks to @sbgrid.bsky.social for inviting us to talk about our structure refinement tools for #cryoem - better structures enable better predictions. It was a pleasure to share the work of many talented group members over the years!

youtu.be/g11qEvSmTLs

Pharma CEOS Speaking Up, Damn It

www.science.org/content/blog...

Issues · biopython/biopython Official git repository for Biopython (originally converted from CVS) - Issues · biopython/biopython

We happily welcome contributions! Check our open issues for ideas on where to start and if you have any questions about how to go about it, etc, just ask.

github.com/biopython/bi...

Inverse problems with experiment-guided AlphaFold Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conf...

📢 New preprint, lead by Alex Bronstein, @sankethvedula.bsky.social and colleagues:
Guiding AlphaFold with experimental data.

This approach generates conformational ensembles guided by NMR, X-ray (or whatever) data. I am thrilled to tackle lots of exciting problems with it!
arxiv.org/abs/2502.09372